lrp_3.0.74

Update task descriptions (#402)

• updated description to wdl files in task Alignment, Assembly, and Preprocessing

• updated description to wdl files in task Transcriptomics

• updated description to wdl files in task QC

• updated description to wdl files in task Utility

• updated description to wdl files in task VariantCalling

• fixes to pass miniwdl validation

• fixes to pass womtool validation

• Update wdl/tasks/QC/Fingerprinting.wdl

• Update wdl/tasks/Utility/ONTUtils.wdl

Co-authored-by: Steve Huang shuang@broadinstitute.org

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com
Co-authored-by: Steve Huang shuang@broadinstitute.org

lrp_3.0.73

development docs draft (#396)

• development docs draft

• added intro for docker_style_guide.md

• add to docker_style_guide.md

• add to wdl_style_guide.md

• renamed dev_guide to development_guide

• rewrote overview, added visuals for directory structure

• Minor fixes, Added Workflow Deployment in README.md

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.72

Fix for Repo Git Page action yml (#398)

• added make docs dir if not exist

• add graphviz as an installation requirement

• switching to mac environment

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.71

Automatically Generate Repository Git Page (#391)

• add git page action

• Add scripts to create dot and png files for workflows

• Add scripts to add png link to md

• Add mkdocs.yml file

• changed png link to be relative path instead of absolute.

• Added script to add header to wdl markdown, and remove task info from wdl workflow markdown

• edited wdlviz.py to add the option to name the output file by a specified name, edited create_wdl_visual.py to use wdl basename for dot file

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.70

New workflows to deal with ONT flowcells that have multiple basecall directories (#325)

• one workflow that essentially copies the current ONTFlowcell, but aims at a basecall directory
• one workflow that plays the role of ONTFlowcell, but actually aggregates results from the WF above

lrp_3.0.69

add miniwdl and shellcheck installation to cd.yml (#397)

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.68

reheader FP vcfs from full hg38 to no_alt (#344)

lrp_3.0.67

Move wdl files to central directory called wdl (#393)

• moved wdls to wdl folder, updated testing location for wdl validation

• updated wdl paths in dockstore.yml

• renamed 'deprecated_wdl' to 'deprecated', updated docstore.yml accordingly

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.66

Standardize wdl description (#392)

• standardized pipeline/ONT workflow meta and parameter_meta bocks

• standardized pipeline/pacbio workflow meta and parameter_meta bocks

• standardized pipeline/techAgnostic workflow meta and parameter_meta bocks

---

Co-authored-by: bshifaw bshifaw@broadinstitute.com

lrp_3.0.65

Update hifiasm assembly (only) workflow (#390)

• MAJOR CHANGES:

  • HiFiasm

    • update hifiasm docker
    • formulated resource allocation
    • As requested, pipeline generates alternate contigs as well.
      Note this essentially forces two assemblies on one set of FASTQs, as
      haplotig-generating assemblies and alternate-generating assemblies are
      generated with different options.

  • QUAST

    • update and shrink Quast docker
    • bigger disk for Quast task
    • now supports multiple assemblies being evaluated at the same time

  • It's almost reference-free now:

    • variant calling is no longer offered
    • only depends on a reference (e.g. T2T) for assembly evaluation (Quast)

• MINOR CHANGES:

  • update various tasks
    • optionally compress files when finalizing
    • merge MergeFastqs and MergeFastqGzs into one task
    • more memory for MergeFastqs; uses LOCAL SSD when files are not too large